He may not be the most insane or evil of the Final Fantasy villains but he is the one that is most easy to relate one. He had the most valid motives for his actions as well. Sephiroth, for example, went crazy because he had severe mommy issues and Kefka, while being an evil asshole, is hardly unique since he is basically an expy of the Joker. The fact that Kuja was doing what he did so that he could remain himself makes him a lot different from the rest and he has the distinction of being the first FF villain to have a change of heart at the end.